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Question: Quick Question About Cuff Compare
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gravatar for Jason Serviss
6.4 years ago by
Jason Serviss • 10
Jason Serviss • 10 wrote:
Hi! Just a quick question.... I am trying to use cuffcompare for human data and want to use a Sequence Data (h19). I can only seem to find the fasta files divided by chromosome. If I upload all of these files individually will the program be able to simultaneously use the files (it looks as though there is only space to input 1 file...)? Or do I need to find the whole genome in 1 Sequence Data file? Thanks in advance for your help! Kind Regards, Jason
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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by Jason Serviss • 10
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Jason, Are you using the public main Galaxy instance at http://main.g2.bx.psu.edu usegalaxy.org)? The hg19 database can be used as a "locally cached" reference genome with the Cuff* RNA-seq tools, so there isn't any need to load external fasta files. If you do decide to use a custom genome in the future (a different genome), individual chromosomes can be merged with the tool "Text Manipulation -> Concatenate datasets". More help with format is on our wiki: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Thanks, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
6.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Jason, The short answer is that the database is interpreted from the database assignment of the inputs to the tool. Have you seen our RNA-seq tutorial? It may answer some of the other questions. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k
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